History Analysis / LEGOGenetics

What is interesting about these genes is that they are ''exactly'' as modular as this would make it seem. The Hox genes do not code for the structures
they build; they only tell the body that the "genetic pathway"[[note]]the genetic equivalent of an .exe file, basically[[/note]] with this particular flag should be executed at this particular place, with these particular settings. This system is quite flexible: like a really good or really bad contractor, when the blueprints ask the body to build something odd and the measurements its told to use don't quite add up, [[MacGyvering it just makes it work as best it can]].

--> do(LAB,PB,DFD,SRC,ANTP,UBX,ABD-A,ABD-B)

--> build(top_of_head),build(limbs(short)[[note]]limb.type defaults to "antennae"[[/note]]),build(brain_eye

--> build(mouth), build(larynx))

--> build(limbs))

--> build(limbs(long)))

-->build(abdomen_a))

-->build(abdomen_b))

The ramifications of this "eh, close enough" method of body assembly might be obvious at this point to anyone who has played with a Mr.Potato Head: one common mutation in fruit flies creates a SequenceBreaking error by moving ANTP to run before SCR. This sets the normal call for the previous and all following limbs to be legs, when the last set of limbs declared are ''supposed'' to be antenna. [[BodyHorror The result is a fruit fly with perfectly formed legs on its head instead of antenna.]] Another duplicates the ABD-A call: this gives you a fly with an extra body segment. Essentially, when the Hox genes are altered randomly, BodyHorror ensues because a developing embryo or creature undergoing {{Metamorphosis}} will build whatever the Hox genes and the gene pathways they point to tell it to build. The vast majority of five legged chickens and one eyed cows are caused by errors in the execution of the Hox genes; essentially the biological equivalent of a GameBreakingBug or KillScreen.

A good way to understand why the Hox genes are so important is thinking of DNA as exactly what it is: a wetware operating system with all of the convoluted strangeness you would expect of an open source project a few billion years old. In this analogy, the Hox genes are the DOS- the part of DNA that makes DNA able to read, organize, and execute particular sections of DNA based on the cell's position in the body, and functions ''very'' similarly to "syntax calls" in computer code, The most fundamental purpose of the Hox genes is to form the Homeobox; the genetic equivalent of a ".init file" for both an organism and the individual cell. This a short[[note]]generally only about 180 base pairs long[[/note]] sequence of genes loosely reflecting the organism's actual structure from head to tail, each chunk of which triggers a particular "programmed" set of genes flagged by a matching ~6 nucleotide long sequence[[note]]Think of it like a search of a digital photo album displaying all pictures tagged "beach"[[/note]].

Translating this into pseudo code, a fruitfly would read roughly something like this:

It should be noted that gene therapy, the alteration, addition or removal of existing genes in an adult organism, [[TruthInTelevision exists]]. Yes, we no longer need the more atrocious method of Eugenics to eradicate debilitating genetic diseases. However, it can be more problematic than presented in fiction, and can wear off after a little while. Additionally, it normally requires very complicated surgery (or the use of gutted viruses) to carry out; you can't simply inject some foreign DNA into your blood and wait for the mutations to take place. However, an evidence for the plausibility of gene therapy lies in the existence of [[http://en.wikipedia.org/wiki/Endogenous_retrovirus Endogenous retrovirus]] DNA. One of our ancestors got infected by a retrovirus, which made its way into the said ancestor's germ cells. Bingo! Now his/her children inherit the virus DNA with the parent DNA, until this day. Some of the endogenous retrovirus DNA has since mutated and became junk DNA, but some of those viruses are actually still active and facilitating mutations and evolution, for better or for worse (like helping the embryo implant in the womb, or playing a role in several diseases).

A good way to understand why the Hox genes are so important is thinking of DNA as exactly what it is: a wetware operating system with all of the convoluted strangeness you would expect of an open source project a few billion years old. In this analogy, the Hox genes are the DOS- the part of DNA that makes DNA able to read, organize, and execute particular sections of DNA based on the cell's position in the body, and functions ''very'' similarly to "syntax calls" in computer code, The most fundamental purpose of the Hox genes is to form the [[https://en.wikipedia.org/wiki/Homeobox Homeobox]]; the genetic equivalent of a ".init file" for both an organism and the individual cell. This a short[[note]]generally only about 180 base pairs long[[/note]] sequence of genes loosely reflecting the organism's actual structure from head to tail, each chunk of which triggers a particular "programmed" set of genes flagged by a matching ~6 nucleotide long sequence[[note]]Think of it like a search of a digital photo album displaying all pictures tagged "beach"[[/note]].

For more information, try UsefulNotes.{{Genetics}} or (if you can handle the TechnoBabble) [[Wiki/{{Wikipedia}} The Other Wiki]].

--> build(top_of_head),build(limbs(short)[[note]]limb.type defaults to "antennae"[[/note]]),build(brain_eyes)

In the more distant future, there is also nothing fundamentally preventing you from copying the "instructions" for, say...[[PrettyButterflies butterfly wings]], [[BioAugmentation into the genome of a frog embryo and creating a butterfrog]]. Where the trouble comes in is tweaking the Hox genes to call this "program" at the right time and place in the frogs development- which, as previously noted, can be [[{{Understatement}} slightly complicated]]. And accounting for engineering concerns like the SquareCubeLaw if you want it to actually fly. And then solving the metabolic nightmare of figuring out what extra proteins the butterfrog would need to be able to produce in order to construct said wings successfully. And then figuring out how to make those proteins not kill the butterfrog. [[GoneHorriblyWrong And how to make swarms of butterfrogs NOT hunger for human flesh.]]

-->everything before this is "head"''

-->everything after this is thorax''

A good way to understand why the Hox genes are so important is thinking of DNA as exactly what it is: a wetware operating system with all of the convoluted strangeness you would expect of an open source project a few billion years old. In this analogy, the Hox genes are the DOS- the part of DNA that makes DNA able to read, organize, and execute particular sections of DNA based on the cells position in the body, and functions ''very'' similarly to "syntax calls" in computer code, The most fundamental purpose of the Hox genes is to form the [[https://en.wikipedia.org/wiki/Homeobox Homeobox]]; the genetic equivalent of a ".init file" for both an organism and the individual cell. This a short[[note]]generally only about 180 base pairs long[[/note]] sequence of genes loosely reflecting the organism's actual structure from head to tail, each chunk of which triggers a particular "programmed" set of genes flagged by a matching ~6 nucleotide long sequence[[note]]Think of it like a search of a digital photo album displaying all pictures tagged "beach"[[/note]].

In the more distant future, there is also nothing fundamentally preventing you from copying the "instructions" for, say...[[PrettyButterflies butterfly wings]], [[BioAugmentation into the genome of a frog embro and creating a butterfrog]]. Where the trouble comes in is tweaking the Hox genes to call this "program" at the right time and place in the frogs development- which, as previously noted, can be [[{{Understatement}} slightly complicated]]. And accounting for engineering concerns like the SquareCubeLaw if you want it to actually fly. And then solving the metabolic nightmare of figuring out what extra proteins the butterfrog would need to be able to produce in order to construct said wings successfully. And then figuring out how to make those proteins not kill the butterfrog. [[GoneHorriblyWrong And how to make swarms of butterfrogs NOT hunger for human flesh.]]

Further than that, once the Hox genes are fully decoded and well understood, the only thing really preventing MixAndMatchCritters is a lot of debugging on the genetic code that you copy and paste together out of [[OurDragonsAreDifferent monitor lizard, bat, and bombarder beetle]] DNA, and the ethics of CreatingLife knowing that it might take dozens, or perhaps hundreds of [[FlawedPrototype beta attempts doomed to live a short and unpleasant life]] to work out the kinks in your bad coding.

Research and experimentation into these genes and the [[JustThinkOfThePotential stagering potential they present]] is somewhat young, and warrants careful handling by potentially invoking 5, possibly 6, of the [[ScaleOfScientificSins Scientific Sins]] simultaneously. What ''has'' been learned so far is that hox genes are potentially the most important, and some of the oldest, genes in life as we know it.

This trope gets even stranger when the genes in question come from somewhere besides Earth. DNA is not just "genetic material." It's a specific molecule that we humans, and almost every living thing on Earth, use. It's one of boundless possible candidates for the job. Viruses may use DNA or its sister RNA for their genome. There's no reason to think extraterrestrial genetic material should be the same as ours. Additionally, DNA contains lots of special little sequences besides genes. These include viruses that simply hopped onto our DNA and get copied with it (endogenous retroviruses), sequences which are apparently just "junk" we can't get rid of, and sequences which tell cells how often to turn on each gene and when to shut it down. This also requires that almost all living cells on Earth interpret a gene the same way. That's the genetic code; almost all cells interpret a particular sequence of three "rungs" to mean the same amino acid when they turn the gene on and start making protein. Yet when the plot demands it, an alien has DNA and all the ancillary stuff to be compatible with our genetic heritage. That's so absurdly improbable that if an organism from another planet were to have DNA at all, rather than some other possible molecule, most scientists would immediately start wondering if we had a common origin (or scream "Hoax!") In fiction, aliens have DNA and interpret it just as things which evolved on Earth do. NoBiochemicalBarriers indeed! Just slap it into our cells and away we go making a HalfHumanHybrid and more.

The fourth type are the hox genes, and they, plain and simple, are what make any multicellular life more complicated than a jellyfish possible.

The Hox genes are an extraordinarily old chunk of dna which seems to date back to the first organism with proto-limbs and a vague concept of bilateral symmetry. They are found virtually unaltered in all branches of complex life, and as best we understand them, they serve as the basic toolkit all complex organisms use for assembling various types of tissues, and generating, maintaining, and regenerating a body plan. These are the genes that tell the body things like how many limbs it should have, where they should be placed, how to assemble its scales, skin, feathers, and/or fur, and what colors these should be. They are the reason that you have ten fingers and ten toes, and none of them are on your head. If you ''have'' more than ten fingers and/or toes, and/or if any of them ''are'' on your head, you can probably thank the hox genes for ''that'', too. These are, in essence, the bricks for playing Lego Genetics.

A good way to understand why the hox genes are so important is thinking of DNA as exactly what it is: a wetware operating system with all of the convoluted strangeness you would expect of an open source project a few billion years old. In this analogy, the hox genes are the DOS- the part of DNA that makes DNA able to read, organize, and execute particular sections of DNA based on the cells position in the body, and functions ''very'' similarly to "syntax calls" in computer code, The most fundamental purpose of the hox genes is to form the [[https://en.wikipedia.org/wiki/Homeobox Homeobox]]; the genetic equivalent of a ".init file" for both an organism and the individual cell. This a short[[note]]generally only about 180 base pairs long[[/note]] sequence of genes loosely reflecting the organism's actual structure from head to tail, each chunk of which triggers a particular "programmed" set of genes flagged by a matching ~6 nucleotide long sequence[[note]]Think of it like a search of a digital photo album displaying all pictures tagged "beach"[[/note]].

What is interesting about these genes is that they are ''exactly'' as modular as this would make it seem. The hox genes do not code for the structures

The ramifications of this "eh, close enough" method of body assembly might be obvious at this point to anyone who has played with a Mr.Potato Head: one common mutation in fruit flies creates a SequenceBreaking error by moving ANTP to run before SCR. This sets the normal call for the previous and all following limbs to be legs, when the last set of limbs declared are ''supposed'' to be antenna. [[BodyHorror The result is a fruit fly with perfectly formed legs on its head instead of antenna.]] Another duplicates the ABD-A call: this gives you a fly with an extra body segment. Essentially, when the hox genes are altered randomly, BodyHorror ensues because a developing embryo or creature undergoing {{Metamorphosis}} will build whatever the hox genes and the gene pathways they point to tell it to build. The vast majority of five legged chickens and one eyed cows are caused by errors in the execution of the hox genes; essentially the biological equivalent of a GameBreakingBug or KillScreen.

The JustThinkOfThePotential sets in with this: All organisms use this same basic template, and tweaks in what the hox genes activate are what leads to whether a creature has feathers or scales, hands or fins. In many cases ancestral traits are still found buried in DNA- it is simply that the organism's hox genes are no longer linked to those now useless chunks of DNA, and they are essentially junk, never to be expressed. For just one example of the real-world implications of the Hox genes on the TwentyMinutesIntoTheFuture future front, numerous scientists have suggested that a pseudo-dinosaur could be reverse engineered out of a bird by tweaking its hox genes. Birds retain the genes for saurian jaws and teeth and clawed hands, and experiments have shown that is a fairly simple matter of artificially activating these sequences and deactivating the bird sequences at the right time in embryo development to create a creature that bears a startling resemblance to an embryonic dinosaur.[[note]]None of these have been allowed to develop past the early embryonic stage due to ethical concerns, for the record.[[/note]]

In the more distant future, there is also nothing fundamentally preventing you from copying the "instructions" for, say...[[PrettyButterflies butterfly wings]], [[BioAugmentation into the genome of a frog embro and creating a butterfrog]]. Where the trouble comes in is tweaking the hox genes to call this "program" at the right time and place in the frogs development- which, as previously noted, can be [[{{Understatement}} slightly complicated]]. And accounting for engineering concerns like the SquareCubeLaw if you want it to actually fly. And then solving the metabolic nightmare of figuring out what extra proteins the butterfrog would need to be able to produce in order to construct said wings successfully. And then figuring out how to make those proteins not kill the butterfrog. [[GoneHorriblyWrong And how to make swarms of butterfrogs NOT hunger for human flesh.]]

Further than that, once the Hox genes are fully decoded and well understood, the only thing really preventing MixAndMatchCritters is a lot of debugging on the genetic code that you copy and paste together out of [[OurDragonsAreDifferent monitor lizard, bat, and bombarder beetle]] dna, and the ethics of CreatingLife knowing that it might take dozens, or perhaps hundreds of [[FlawedPrototype beta attempts doomed to live a short and unpleasant life]] to work out the kinks in your bad coding.

The Hox genes are an extraordinarily old chunk of dna which seems to date back to the first organism with proto-limbs and a vague concept of bilateral symmetry. They are found virtually unaltered in all branches of complex life, and as best we understand them, they serve as the basic toolkit all complex organisms use as a generic genetic toolkit for assembling various types of tissues, and generating, maintaining, and regenerating a body plan. These are the genes that tell the body things like how many limbs it should have, where they should be placed, how to assemble its scales, skin, feathers, and/or fur, and what colors these should be. They are the reason that you have ten fingers and ten toes, and none of them are on your head. If you ''have'' more than ten fingers and/or toes, and/or if any of them ''are'' on your head, you can probably thank the hox genes for ''that'', too. These are, in essence, the bricks for playing Lego Genetics.

In essence, the potential for PlayingWithSyringes is there.

In the more distant future, there is also nothing fundamentally preventing you from copying the "instructions" for, say...[[PrettyButterflies butterfly wings]], [[BioAugmentation into the genome of a frog embro and creating a butterfrog]]. Where the trouble comes in is tweaking the hox genes to call this "program" at the right time and place in the frogs development- which, as previously noted, can be [[{{Understatement}} slightly complicated]]. And accounting for engineering concerns like the SquareCubeLaw if you want it to actually fly. And then solving the metabolic nightmare of figuring out what extra proteins the butterfrog would need to be able to produce in order to construct said wings successfully. And then figure out how to make those proteins not kill the butterfrog. [[GoneHorriblyWrong And how to make swarms of butterfrogs NOT hunger for human flesh.]]

In the more distant future, there is also nothing fundamentally preventing you from copying the "instructions" for, say...[[PrettyButterflies butterfly wings]], [[BioAugmentation into the genome of a frog embro and creating a butterfrog]]. Where the trouble comes in is tweaking the hox genes to call this "program" at the right time and place in the frogs development- which, as previously noted, can be [[{{Understatement}} slightly complicated]]. And accounting for engineering concerns like the SquareCubeLaw if you want it to actually fly. And then solve the metabolic nightmare of figuring out what extra proteins the butterfrog would need to be able to produce in order to construct said wings successfully. And how to make those proteins not kill the butterfrog. [[GoneHorriblyWrong And then how to make swarms of butterfrogs NOT hunger for human flesh.]]

In the more distant future, there is also nothing fundamentally preventing you from copying the "instructions" for, say...[[PrettyButterflies butterfly wings]], [[BioAugmentation into the genome of a frog embro and creating a butterfrog]]. Where the trouble comes in is tweaking the hox genes to call this "program" at the right time and place in the frogs development- which, as previously noted, can be [[{{Understatement}} slightly complicated]]. And account for engineering concerns like the SquareCubeLaw if you want it to actually fly. And then solve the metabolic nightmare of figuring out what extra proteins the butterfrog would need to be able to produce in order to construct said wings successfully. And how to make those proteins not kill the butterfrog. [[GoneHorriblyWrong And then how to make swarms of butterfrogs NOT hunger for human flesh.]]

The Hox genes are an extraordinarily old chunk of dna which seems to date back to the first organism with proto-limbs and bilateral symmetry. They are found virtually unaltered in all branches of complex life, and as best we understand them, they serve as the basic toolkit for generating a body plan. These are, in essence, the bricks for playing Lego Genetics.

Research and experimentation in this field is somewhat young, and warrants careful handling by potentially invoking 5, possibly 6, of the [[ScaleOfScientificSins Scientific Sins]] simultaneously. What ''has'' been learned so far is that these genes represent fundamental "syntax calls" in the same sense as computer code. These are the genes that tell the body things like how many limbs it should have, where they should be placed, how to assemble its scales, feathers, or fur, and what colors these should be. All other genes seem to either code for chemical assemblies, or serve as on and off switches for the hox genes. All complex organisms on earth also seem to have the genetic equivalent of a ".init file" called a [[https://en.wikipedia.org/wiki/Homeobox Homeobox]], a short[[note]]generally only about 180 base pairs long[[/note]] sequence of genes loosely reflecting its actual structure from head to tail, each chunk of which triggers a particular "programmed" sequence of hox genes. Translating this into pseudo code, the homeobox of a fruitfly would read roughly something like this:

-->while(head)
--->do(build(mouth),build(top_of_head),right_left(build(antennas)), right_left(build(brain_eyes))
-->do(build(head))
-->while(thorax)
--->do(right_left(build_front_legs))
-->do(build(thorax))
-->do(right_left(build(wings))
-->do(right_left(build(middle_legs))
-->do(right_left(build(rear_legs))
-->do(build(abdomen_a))
-->do(build(abdomen_b))

the build(front_leg) function might look something like
-->do(build(leg_section))
-->do(build(joint))
-->do(build(leg_section))
-->do(build(joint))
--->*This is the long part of the leg:*
-->do(build(leg_section))
-->repeat
-->repeat
-->repeat
-->repeat
-->do(build(joint))
-->do(build(foot))

What is interesting about these genes is that they are exactly as modular as this would make it seem. One common mutation in fruit flies replaces the Build(antenna) call with a call to Build(front_leg)[[BodyHorror The result is a fruit fly with perfectly formed legs on its head instead of antenna.]] Another duplicates the Build(abdomen_a) gene- this gives you a fly with an extra body segment. Similarly, when someone is born with six perfectly formed fingers, its because their build(fingers) section had one extra repeat tag. Like a really good or really bad contractor, when the blueprints ask it to build something odd and the measurements its told to use don't quite add up, it just makes it work as best it can.

The JustThinkOfThePotential sets in with this: given that all organisms use this same basic template, with tweaks in execution of the "programs" rather than the hox genes themselves making feathers instead of scales or hands instead of fins, the only thing preventing copying the "instructions" for, say, butterfly wings into the genome of a frog and calling this program at the right time an place in the frogs development, is the SquareCubeLaw. And the metabolic nightmare of figuring out what extra proteins the butterfrog would need to be able to produce in order to construct said wings successfully. And then what you would have to tweak to make those proteins not kill the butterfrog. [[GoneHorriblyWrong And then how to make the butterfrog not hunger for human flesh.]] Theoretically, however, once the Hox genes are fully decoded and well understood, the only thing preventing MixAndMatchCritters is a lot of debugging on the genetic code that you copy and paste together out of [[OurDragonsAreDifferent monitor lizard, bat, and bombarder beetle]] dna.

The JustThinkOfThePotential set in with this: given that all organisms use this same basic template, with tweaks in execution of the "programs" rather than the hox genes themselves making feathers instead of scales or hands instead of fins, the only thing preventing copying the "instructions" for, say, butterfly wings into the genome of a frog and calling this program at the right time an place in the frogs development, is the SquareCubeLaw. And the metabolic nightmare of figuring out what extra proteins the butterfrog would need to be able to produce in order to construct said wings successfully. And then what you would have to tweak to make those proteins not kill the butterfrog. [[GoneHorriblyWrong And then how to make the butterfrog not hunger for human flesh.]] Theoretically, however, once the Hox genes are fully decoded and well understood, the only thing preventing MixAndMatchCritters is a lot of debugging on the genetic code that you copy and paste together out of [[OurDragonsAreDifferent monitor lizard, bat, and bombarder beetle]] dna.

While research and experimentation in this field is somewhat young, and warrants careful handling by potentially invoking 5, possibly 6, of the [[ScaleOfScientificSins Scientific Sins]] simultaneously. What ''has'' been learned so far is that these genes represent fundamental "syntax calls" in the same sense as computer code. These are the genes that tell the body things like how many limbs it should have, where they should be placed, how to assemble its scales, feathers, or fur, and what colors these should be. All other genes seem to either code for chemical assemblies, or serve as on and off switches for the hox genes. All complex organisms on earth also seem to have the genetic equivalent of a ".init file" called a [[https://en.wikipedia.org/wiki/Homeobox Homeobox]], a short[[note]]generally only about 180 base pairs long[[/note]] sequence of genes loosely reflecting its actual structure from head to tail, each chunk of which triggers a particular "programmed" sequence of hox genes. Translating this into pseudo code, the homeobox of a fruitfly would read roughly something like this:

The JustThinkOfThePotential set in with this: given that all organisms use this same basic template with tweaks in execution to get feathers instead of scales or hands instead of fins, the only thing preventing copying the "instructions" for, say, butterfly wings into the genome of a frog, and calling them at the right point is the SquareCubeLaw and metabolic nightmare of figuring out what extra proteins the frog would need in order to construct said wings successfully. Theoretically, however, once the Hox genes are fully decoded and well understood, the only thing preventing MixAndMatchCritters is a lot of debugging on the genetic code that you copy and paste together out of [[OurDragonsAreDifferent monitor lizard, bat, and bombarder beetle]] dna.

For more information, try UsefulNotes.{{Genetics}} or (if you can handle the TechnoBabble) [[Wiki/{{Wikipedia}} The Other Wiki]].

This trope gets even stranger when the genes in question come from somewhere besides Earth. DNA is not just "genetic material." It's a specific molecule that we humans, and almost every living thing on Earth, use. It's one of boundless possible candidates for the job. Viruses may use DNA or its sister RNA for their genome, and there have even been some (highly controversial) studies that indicate there may be microorganisms that use Arsenic in their genetic material where we use Phosphorus. There's no reason to think extraterrestrial genetic material should be the same as ours. Additionally, DNA contains lots of special little sequences besides genes. These include viruses that simply hopped onto our DNA and get copied with it (endogenous retroviruses), sequences which are apparently just "junk" we can't get rid of, and sequences which tell cells how often to turn on each gene and when to shut it down. This also requires that almost all living cells on Earth interpret a gene the same way. That's the genetic code; almost all cells interpret a particular sequence of three "rungs" to mean the same amino acid when they turn the gene on and start making protein. Yet when the plot demands it, an alien has DNA and all the ancillary stuff to be compatible with our genetic heritage. That's so absurdly improbable that if an organism from another planet were to have DNA at all, rather than some other possible molecule, most scientists would immediately start wondering if we had a common origin (or scream "Hoax!") In fiction, aliens have DNA and interpret it just as things which evolved on Earth do. NoBiochemicalBarriers indeed! Just slap it into our cells and away we go making a HalfHumanHybrid and more.